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(-) Description

Title :  STRUCTURE OF DOUBLE MUTANT, D164N, E78H OF KUMAMOLISIN-AS
 
Authors :  M. Li, A. Wlodawer, A. Gustchina, T. Nakayama
Date :  02 Jun 05  (Deposition) - 23 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  D164N, E78H, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Okubo, M. Li, M. Ashida, H. Oyama, A. Gustchina, K. Oda, B. M. Dunn, A. Wlodawer, T. Nakayama
Processing, Catalytic Activity And Crystal Structures Of Kumamolisin-As With An Engineered Active Site.
Febs J. V. 273 2563 2006
PubMed-ID: 16704427  |  Reference-DOI: 10.1111/J.1742-4658.2006.05266.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KUMAMOLISIN-AS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ALICYCLOBACILLUS SENDAIENSIS
    Organism Taxid: 192387

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:316 , ILE A:317 , GLY A:334 , GLY A:336 , ASP A:338 , HOH A:1001BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREASP B:316 , ILE B:317 , GLY B:334 , GLY B:336 , ASP B:338 , HOH B:2001BINDING SITE FOR RESIDUE CA B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZVK)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:180 -Pro A:181
2Val A:250 -Pro A:251
3Ile A:330 -Tyr A:331
4Phe B:180 -Pro B:181
5Val B:250 -Pro B:251
6Ile B:330 -Tyr B:331

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZVK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZVK)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZVK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:355
 aligned with Q8GB88_9BACL | Q8GB88 from UniProtKB/TrEMBL  Length:553

    Alignment length:355
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542     
         Q8GB88_9BACL   193 TAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGEVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALLPS 547
               SCOP domains d1zvka_ A: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1zvkA00 A:4-358  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...........eeeeee.....hhhhhhhhhhhh......eeeee..............hhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhh.......eeee...ee.hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh.........ee.......eeeeeeeeeee..eeeeeee..hhhhhh....ee......hhhhh................ee..eeee.hhhhheeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.ee.............................eehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zvk A   4 TAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGHVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGNSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALLPS 358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353     


Chain B from PDB  Type:PROTEIN  Length:355
 aligned with Q8GB88_9BACL | Q8GB88 from UniProtKB/TrEMBL  Length:553

    Alignment length:355
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542     
         Q8GB88_9BACL   193 TAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGEVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGDSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALLPS 547
               SCOP domains d1zvkb_ B: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1zvkB00 B:4-358  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) -------------------------------------------------------------------------Peptidase_S8-1zvkB01 B:77-337                                                                                                                                                                                                                                        --------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------Peptidase_S8-1zvkB02 B:77-337                                                                                                                                                                                                                                        --------------------- Pfam domains (2)
         Sec.struct. author .eehhhhhhhhh...........eeeeee.....hhhhhhhhhhhh......eeeee.............hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh......eeee...ee.hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh.........ee.......eeeeeeeeeee..eeeeeee..hhhhhh....ee......hhhhh................ee..eeee.hhhheeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.ee.............................eehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zvk B   4 TAYTPLDVAQAYQFPEGLDGQGQCIAIIELGGGYDEASLAQYFASLGVPAPQVVSVSVDGASNQPTGDPSGPDGHVELDIEVAGALAPGAKFAVYFAPNTDAGFLDAITTAIHDPTLKPSVVSISWGGPEDSWTSAAIAAMNRAFLDAAALGVTVLAAAGNSGSTDGEQDGLYHVDFPAASPYVLACGGTRLVASGGRIAQETVWNDGPDGGATGGGVSRIFPLPAWQEHANVPPSANPGASSGRGVPDLAGNADPATGYEVVIDGEATVIGGTSAVAPLFAALVARINQKLGKAVGYLNPTLYQLPADVFHDITEGNNDIANRAQIYQAGPGWDPCTGLGSPIGVRLLQALLPS 358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8GB88_9BACL | Q8GB88)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8GB88_9BACL | Q8GB88: 1sio 1siu 1sn7 1zvj 4ne7

(-) Related Entries Specified in the PDB File

1s1o WILD TYPE COMPLEXED WITH AN INHIBITOR
1s1u E78H MUTANT
1sn7 APO STRUCTURE
1zvk D146N,E78H MUTANT